scOrange Blog


Author: Ajda Pretnar, Oct 4, 2018

Cell Clustering and Cluster Analysis

Discovering new marker genes is a core step in the analysis of single-cell sequencing data. Use Louvain clustering to find cell populations and visualize the cell landscape in a t-SNE projection. Examine the contents of each cluster by finding differentially expressed genes and their related functions according to the Gene Ontology database.


Author: Ajda Pretnar, Oct 3, 2018

Exploring cell populations with t-SNE

Single-cell RNA sequencing protocols enable measuring the transcriptome on a single-cell resolution. We explore the different cell types in a blood sample by a integrating existing knowledge on known marker genes and a t-SNE visualization, focusing on interactive exploration of data.